Contacts of the strand formed by residues 57 - 63 (chain G) in PDB entry 4CDC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 57 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334E ALA* 5.7 3.6 - - - -
338E LEU* 5.1 10.9 - - - +
49G THR* 4.9 9.0 - - - -
50G ALA 3.2 8.1 - - - -
51G TYR* 4.5 6.3 - - - -
55G GLY 4.0 3.0 + - - -
56G ASN* 1.3 75.4 - - - +
58G GLY* 1.3 60.7 + - - +
72G LEU* 3.6 9.3 - - - +
73G ASN 5.0 1.7 + - - -
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Residues in contact with GLY 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G THR* 3.5 5.7 - - - +
50G ALA* 2.6 30.6 + - - +
57G SER* 1.3 77.4 - - - +
59G HIS* 1.3 83.3 + - - -
71G VAL 3.5 12.6 - - - -
72G LEU* 3.6 4.2 - - - +
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Residues in contact with HIS 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G ASP* 3.1 37.0 - - - +
49G THR* 5.0 2.2 - - - -
50G ALA* 3.9 3.1 - - - +
58G GLY* 1.3 88.0 + - - -
60G PHE* 1.3 64.9 + - - +
70G ILE* 3.5 3.6 - - - +
71G VAL* 2.9 39.3 + - + +
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Residues in contact with PHE 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G TYR* 3.8 15.0 - + - -
11G LEU* 3.7 31.0 - - + -
12G LEU* 3.7 22.9 - - + -
44G LEU* 3.9 17.7 - - + -
45G GLN 3.3 27.6 - - - -
47G LEU 3.7 14.3 - - - +
48G ASP* 3.1 36.8 + - - +
49G THR 3.4 23.8 - - - -
50G ALA* 4.6 0.4 - - + -
59G HIS* 1.3 77.2 - - - +
61G THR* 1.3 70.7 + - - +
68G PHE* 5.6 0.4 - - + -
69G GLU 3.2 13.0 - - - +
70G ILE* 3.8 16.8 - - + -
326H GLY 5.4 0.3 - - - +
327H PHE* 4.1 3.3 - - - +
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Residues in contact with THR 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G LEU* 4.5 0.2 - - - -
60G PHE* 1.3 84.7 - - - +
62G ILE* 1.3 74.0 + - - +
63G ILE* 4.5 2.2 - - + -
68G PHE* 3.2 5.0 - - - +
69G GLU* 3.0 40.1 + - + +
280H TYR* 3.7 31.4 - - + +
323H TYR* 3.5 8.8 - - + -
326H GLY 5.1 1.6 - - - -
327H PHE* 3.7 13.1 - - - +
328H TYR 2.9 28.9 + - - -
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G CYS 4.1 5.2 - - - +
7G THR 3.7 32.1 - - - +
8G TYR* 3.8 21.6 - - + +
11G LEU* 3.7 19.4 - - + +
60G PHE* 4.3 2.4 - - - -
61G THR* 1.3 88.8 + - - +
63G ILE* 1.3 60.1 + - - +
64G TYR 3.6 17.5 - - - +
67G GLY 3.1 20.0 - - - +
81G PHE* 4.0 17.9 - - + -
323H TYR* 3.6 2.8 - - - -
328H TYR* 3.2 43.5 + - + +
375I PRO* 4.7 3.6 - - + -
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G THR* 4.5 2.9 - - + +
62G ILE* 1.3 73.4 - - - +
64G TYR* 1.3 67.2 + - - +
66G GLN* 3.0 20.9 + - + +
67G GLY 2.9 13.5 + - - +
68G PHE* 3.6 31.6 - - - +
69G GLU* 3.9 8.7 - - + +
78G PHE* 3.9 9.9 - - + -
278H PHE* 4.3 18.4 - - + -
280H TYR* 4.2 15.3 - - + -
281H LEU* 3.9 44.0 - - + -
323H TYR* 3.4 19.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il